Genome Sequences of 26 White Sucker Hepatitis B Virus Isolates from White Sucker, Catostomus commersonii, Inhabiting Transboundary Waters from Alberta, Canada, to the Great Lakes, USA.
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ABSTRACT:
SUBMITTER: Adams CR
PROVIDER: S-EPMC7975886 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The white sucker Catostomus commersonii is a freshwater teleost often utilized as a resident sentinel. Here, we sequenced the full genome of a hepatitis B-like virus that infects white suckers from the Great Lakes Region of the United States. Dideoxy sequencing confirmed that the white sucker hepatitis B virus (WSHBV) has a circular genome (3,542 bp) with the prototypical codon organization of hepadnaviruses. Electron microscopy demonstrated that complete virions of approximately 40 nm were present in the plasma of infected fish. Compared to avi- and orthohepadnaviruses, sequence conservation of the core, polymerase, and surface proteins was low and ranged from 16 to 27% at the amino acid level. An X protein homologue common to the orthohepadnaviruses was not present. The WSHBV genome included an atypical, presumptively noncoding region absent in previously described hepadnaviruses. Phylogenetic analyses confirmed WSHBV as distinct from previously documented hepadnaviruses. The level of divergence in protein sequences between WSHBV and other hepadnaviruses and the identification of an HBV-like sequence in an African cichlid provide evidence that a novel genus of the family Hepadnaviridae may need to be established that includes these hepatitis B-like viruses in fishes. Viral transcription was observed in 9.5% (16 of 169) of white suckers evaluated. The prevalence of hepatic tumors in these fish was 4.9%, and only 2.4% of fish were positive for both virus and hepatic tumors. These results are not sufficient to draw inferences regarding the association of WSHBV and carcinogenesis in white sucker.We report the first full-length genome of a hepadnavirus from fishes. Phylogenetic analysis of this genome indicates divergence from genomes of previously described hepadnaviruses from mammalian and avian hosts and supports the creation of a novel genus. The discovery of this novel virus may better our understanding of the evolutionary history of hepatitis B-like viruses of other hosts. In fishes, knowledge of this virus may provide insight regarding possible risk factors associated with hepatic neoplasia in the white sucker. This may also offer another model system for mechanistic research.
| S-EPMC4645335 | biostudies-literature
Project description:Hepatitis B viruses belong to a family of circular, double-stranded DNA viruses that infect a range of organisms, with host responses that vary from mild infection to chronic infection and cancer. The white sucker hepatitis B virus (WSHBV) was first described in the white sucker (Catostomus commersonii), a freshwater teleost, and belongs to the genus Parahepadnavirus. At present, the host range of WSHBV and its impact on fish health are unknown, and neither genetic diversity nor association with fish health have been studied in any parahepadnavirus. Given the relevance of genomic diversity to disease outcome for the orthohepadnaviruses, we sought to characterize genomic variation in WSHBV and determine how it is structured among watersheds. We identified WSHBV-positive white sucker inhabiting tributaries of Lake Michigan, Lake Superior, Lake Erie (USA), and Lake Athabasca (Canada). Copy number in plasma and in liver tissue was estimated via qPCR. Templates from 27 virus-positive fish were amplified and sequenced using a primer-specific, circular long-range amplification method coupled with amplicon sequencing on the Illumina MiSeq. Phylogenetic analysis of the WSHBV genome identified phylogeographical clustering reminiscent of that observed with human hepatitis B virus genotypes. Notably, most non-synonymous substitutions were found to cluster in the pre-S/spacer overlap region, which is relevant for both viral entry and replication. The observed predominance of p1/s3 mutations in this region is indicative of adaptive change in the polymerase open reading frame (ORF), while, at the same time, the surface ORF is under purifying selection. Although the levels of variation we observed do not meet the criteria used to define sub/genotypes of human and avian hepadnaviruses, we identified geographically associated genome variation in the pre-S and spacer domain sufficient to define five WSHBV haplotypes. This study of WSHBV genetic diversity should facilitate the development of molecular markers for future identification of genotypes and provide evidence in future investigations of possible differential disease outcomes.
| S-EPMC7918172 | biostudies-literature
Project description:Catostomus commersonii (white sucker) Transcriptome or Gene expression
| PRJNA282680 | ENA
Project description:The relationship between June sucker (Chasmistes liorus, Jordan, 1878) and Utah sucker (Catostomus ardens, Jordan & Gilbert, 1881) has been a matter of controversy since the mid 1900s. Chasmistes liorus is endemic to Utah Lake, UT and has a subterminal mouth adapted for pelagic feeding. Catostomus ardens is widely distributed throughout the Bonneville Basin and Upper Snake River Basin and has a ventral mouth adapted for benthic feeding. Chasmistes has been recognized as a separate ancient genus. Despite being morphologically distinct, no study has successfully identified residual genetic markers that separate these species. Of these studies, several have used a subset of mitochondrial genes, but no study has analyzed the complete mitochondrial genomes (mitogenomes) of these suckers (Pisces: Catostomidae). To further explore the genetic relationships between these species, we report the complete mitogenomes of Chasmistes liorus and Catostomus ardens. DNA was sequenced using an Illumina HiSeq 2500 system and mitogenomes were assembled and annotated using Geneious v. 2021.2 and MitoAnnotator, respectively. The mitogenomes of Chasmistes liorus and Catostomus ardens are both 16,623 bp and are ∼0.072% divergent. We examine the phylogenetic relationship between Chasmistes liorus and Catostomus ardens using 33 mitogenomes, representing 16 species, from Catostomidae. Our data suggest that Chasmistes liorus is sister to Catostomus ardens. Additional samples from multiple localities and/or cohorts of these species will allow us to better resolve the complicated phylogenetic relationships between these species.
| S-EPMC8967188 | biostudies-literature
Project description:The nucleotide sequences of cloned cDNAs encoding the precursors for vasotocin and isotocin have been elucidated by analyzing a lambda gt11 library constructed from poly(A)+ RNA from the hypothalamic region of the teleost fish Catostomus commersoni. Screening of the library was carried out with synthetic oligonucleotide probes deduced from the amino acid sequences of the nonapeptides vasotocin and isotocin. The cDNA nucleotide sequences predict isotocin and vasotocin prohormone precursors each consisting of a signal peptide, a hormone moiety, and a neurophysin-like molecule. However, in comparison to their mammalian counterparts, both fish neurophysins are extended at their C termini by an approximately 30 amino acid sequence with a leucine-rich core segment. These extensions show striking similarities with the glycopeptide moiety (the so-called copeptin) present in mammalian vasopressin precursors, except that they lack the consensus sequence for N-glycosylation. These data suggest that mammalian copeptin is derived from the C terminus of an ancestral neurophysin.
| S-EPMC297597 | biostudies-other
Project description:1. G.l.c. examination of bile alcohols prepared from the sucker Catostomus commersoni Lacépède (family Catostomidae) showed that although 5alpha-cyprinol (5alpha-cholestane-3alpha,7alpha,12alpha,26,27-pentol) was a minor constituent, the principal bile alcohol was an undescribed substance, probably present in the bile as the C-26 sulphate ester, whose i.r., n.m.r. and mass spectra agreed with the structure 5alpha-cholestane-3alpha,7alpha,12alpha,24,26-pentol. 2. M(D) studies suggest that this 5alpha-chimaerol is the 24(+), 25S enantiomer and that 5beta-chimaerol (chimaerol) from Chimaera monstrosa bile also has the 24(+), 25S configuration. These findings imply that bile alcohol biosynthesis in suckers and chimaeras includes stereospecific oxidation of cholesterol at C-26. 3. C. commersoni bile acids (present in minor amounts) probably consist largely of 3alpha,7alpha,12alpha-trihydroxy-5alpha-cholan-24-oic acid (allocholic acid). 4. 5alpha-Chimaerol sulphate and 5alpha-cyprinol sulphate are probably biochemically equivalent as bile salts, and can be considered as arising by parallel evolution.
| S-EPMC1185402 | biostudies-other
Project description:GRACE Terrestrial Water Storage (TWS) provides unique and unprecedented perspectives about freshwater availability and change globally. However, GRACE-TWS records are relatively short for long-term hydroclimatic variability studies, dating back to April 2002. In this paper, we made use of Noah Land Surface Model (LSM), and El Niño-Southern Oscillation (ENSO) data in an autoregressive model with exogenous variables (ARX) to reconstruct a 66-year record of TWS for nine major transboundary river basins (TRBs) in Africa. Model performance was evaluated using standard indicators, including the Nash Sutcliffe Efficiency criteria, cumulative density frequency, standardized residuals plots, and model uncertainty bounds. Temporally, the reconstruction results were evaluated for trend, cycles, and mode of variability against ancillary data from the WaterGAP Model (WGHM-TWS) and GPCC-based precipitation anomalies. The temporal pattern reveals good agreement between the reconstructed TWS, WGHM-TWS, and GPCC, (p-value < 0.0001). The reconstructed TWS suggests a significant declining trend across the northern and central TRBs since 1951, while the southern basins show an insignificant trend. The mode of variability analysis indicates short storage periodicity of four to sixteen-month in the northern basins, while strong intra-annual variability in the central and southern basins. The long-term TWS records provide additional support to Africa's water resources research on hydroclimatic variability and change in shared transboundary water basins.
| S-EPMC6707189 | biostudies-literature
Project description:White sucker hepatitis B virus Genome sequencing and assembly
| PRJNA685065 | ENA
Project description:Oxygen-18 and deuterium analyses of water samples are provided from a regional survey of lakes, wetlands, soil waters, groundwaters, and snowpack samples collected in the Southern Athabasca Oil Sands (SAOS) region, Alberta, Canada, mainly during 2007-2009. Lake, wetland, and river sampling were conducted by helicopter during late summer, capturing conditions close to peak evaporative enrichment. Shallow soil water from the unsaturated zone was also collected in late summer, whereas deeper groundwaters from Quaternary aquifers, Quaternary channels, and uppermost Cretaceous strata, were collected primarily as part of winter drilling programs by industrial partners. Snowpack samples were collected in late March/early April, prior to significant spring melt. This dataset includes 1576 isotopic analyses made on 788 water samples as well as selected isotope mass balance model outputs (lake evaporation/inflow and water yield to lakes). These basic model data are provided to facilitate evaluation of the method as a tool for spatial mapping of water yield and its interannual variability. Details and further discussion on the isotope mass balance approach are provided in "Mapping water yield distribution across the southern Athabasca Oil Sands area: baseline surveys applying isotope mass balance of lakes" (Gibson et al., 2019). Overall, the data are expected to be useful, in comparison with local and regional datasets, for water resource management and planning, including design of monitoring networks and environmental impact assessments for oil sands projects.
| S-EPMC6362867 | biostudies-other